Tradition records that Iain's marriage to the daughter of MacEanruig or MacHenry the 'head man' in Glencoe brought the MacDonalds these Glencoe lands. Glencoe was however an ever hostile environment where people were obliged by the sparseness of the soil to raid and steal cattle from their neighbours.

The MacDonalds alliance to the Stuart cause made them more unpopular with the government. This led to the Massacre of Glencoe (Gaelic: Mort Ghlinne Comhann) in the early hours of the 13th of February 1692, where 38 unarmed MacDonalds were massacred by troops under Robert Campbell of Glenlyon from Clan Campbell. The massacre took place near the village of Glencoe (Gaelic: Gleann Comhann) and in various parts of Glencoe at Inverrigan, Invercoe, Carnoch, Auchnaion and Achtriochtan. Most of the clan, perhaps 300, did escape the initial slaughter only for some to die in the surrounding hills and mountains due to lack of food and shelter as their houses had been burned down.

Memorial at Glencoe

The massacre was ordered upon them because of the Chief's failure to sign an oath of allegiance to King William III of England, Scotland and Ireland before the 1st January 1692. However MacIain had intended to sign the oath but savage snow storms prevented him. Even though his attempt was known to the government they decided an example needed to be made and the massacre went ahead anyway.

The clan's tartan is sold as MacIain/MacDonald of Glencoe but sometimes is often sold as MacDonald of Ardnamurchan through confusion of both clans being known as MacIains. There is a separate tartan known as the MacDonald of Glencoe, it is very different from the MacIan or the Ardnamuchan. This is the proper tartan for Glencoe and was found on the bodies exhumed in the 1800s for burial in consecrated ground. This is an ancient tartan and predates the Highland Clearances.

The Cameron Henry of Penicuik is currently claiming clan chief through ancestry by sept Henry. They are represented by the High Chief of Clan Donald. Currently there are 4 contenders for MacDonald of Glencoe Chiefship.[citation needed]The families descended from James Cameron of Madagascar are as well preparing a claim. It is anticipated that this matter will be settled by Lord Lyon King of Arms in the next few years.[citation needed]